For each sample set, we first provide a summary plot of FST bewteen resistant and susceptible samples across the genome, with FST shown in red and the results of the 200 randomisations shown behind in grey. Windows identified as peaks are highlighted by points, colour-coded by whether they are significantly higher than expected based on the simulations (green) or not (purple). For each significant window (green points), we then provide four additional figures. The first shows the significant (P < 0.01) SNPs found in the region of that window, and their -log10(Pvalue) of association with phenotype. Red points indicate non-synonymous SNPs, blue points indicate all other SNPs. Point shape indicates whether the mutant allele at that SNP is associated with increased (circle) or decreased (triangle) resistance. Dark points in the centre of the plot show SNPs within the significant window, light points on the sides show SNPs in region 10,000 bp either side of the window. The second plot shows the hierarchical cluster of haplotypes in the window, with brackets indicating large haplotype clusters. The third plot shows, each haplotype cluster, indicating the number of haplotypes comprising the cluster (n), the P value of association of the cluster with resistance phenotype, and the SNPs that differentiate that cluster from other haplotypes in the region, colour-coded by type (red = non-synonymous, yellow = synonymous, blue = non-coding). The final figure shows the contingency tables of phenotype association for each haplotype cluster.
Legend
Avrankou_coluzzii_Delta
Baguida_gambiae_Delta
Korle-Bu_coluzzii_Delta
Madina_gambiae_Delta
Obuasi_gambiae_Delta
Baguida_gambiae_PM
Korle-Bu_coluzzii_PM
Madina_gambiae_PM
Obuasi_gambiae_PM
Avrankou_coluzzii_Delta_2R:45413683-45433265
Avrankou_coluzzii_Delta_X:8745589-8778998
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 11 | 22 | 12 |
| dead | 14 | 16 | 4 |
Baguida_gambiae_Delta_2R:33967209-33981960
Baguida_gambiae_Delta_3L:3059554-3112922
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 31 | 21 | 2 |
| dead | 31 | 3 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 37 | 8 | 9 |
| dead | 11 | 21 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 39 | 14 | 1 |
| dead | 28 | 6 | 0 |
Korle-Bu_coluzzii_Delta_2R:28145243-28168331
Korle-Bu_coluzzii_Delta_2R:39682306-39698081
Korle-Bu_coluzzii_Delta_3R:50971406-51021318
Korle-Bu_coluzzii_Delta_X:14653714-14668824
Korle-Bu_coluzzii_Delta_X:14668824-14684264
Korle-Bu_coluzzii_Delta_X:15670884-15702974
Korle-Bu_coluzzii_Delta_X:15702974-15756306
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 52 | 7 | 0 |
| dead | 52 | 30 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 46 | 12 | 1 |
| dead | 69 | 13 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 50 | 9 | 0 |
| dead | 67 | 16 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 48 | 11 | 0 |
| dead | 72 | 11 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 47 | 12 | 0 |
| dead | 65 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 42 | 16 | 1 |
| dead | 77 | 6 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 44 | 13 | 2 |
| dead | 53 | 26 | 4 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 45 | 14 | 0 |
| dead | 75 | 7 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 49 | 10 | 0 |
| dead | 72 | 10 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 30 | 26 | 3 |
| dead | 58 | 24 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 49 | 9 | 1 |
| dead | 69 | 12 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 51 | 8 | 0 |
| dead | 70 | 13 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 31 | 25 | 3 |
| dead | 58 | 24 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 47 | 11 | 1 |
| dead | 69 | 12 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 51 | 8 | 0 |
| dead | 70 | 13 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 13 | 32 | 14 |
| dead | 37 | 35 | 11 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 52 | 7 | 0 |
| dead | 69 | 14 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 53 | 6 | 0 |
| dead | 68 | 15 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 12 | 38 | 9 |
| dead | 38 | 35 | 10 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 52 | 7 | 0 |
| dead | 68 | 14 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 52 | 7 | 0 |
| dead | 69 | 14 | 0 |
Madina_gambiae_Delta_2R:28401363-28416200
Madina_gambiae_Delta_2R:28454838-28474602
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 13 | 33 | 18 |
| dead | 14 | 21 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 8 | 33 | 23 |
| dead | 12 | 20 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 50 | 13 | 1 |
| dead | 26 | 10 | 1 |
Obuasi_gambiae_Delta_2R:28250033-28262588
Obuasi_gambiae_Delta_2R:28262588-28274893
Obuasi_gambiae_Delta_2R:28274893-28289873
Obuasi_gambiae_Delta_2R:28289873-28306606
Obuasi_gambiae_Delta_2R:28306605-28322681
Obuasi_gambiae_Delta_2R:28322681-28337951
Obuasi_gambiae_Delta_2R:28337951-28354693
Obuasi_gambiae_Delta_2R:28354692-28369784
Obuasi_gambiae_Delta_2R:28369784-28391434
Obuasi_gambiae_Delta_2R:28391433-28405240
Obuasi_gambiae_Delta_2R:28405239-28421116
Obuasi_gambiae_Delta_2R:28421116-28439220
Obuasi_gambiae_Delta_2R:28439219-28456407
Obuasi_gambiae_Delta_2R:28456407-28475225
Obuasi_gambiae_Delta_2R:28475225-28496115
Obuasi_gambiae_Delta_2R:28496114-28515482
Obuasi_gambiae_Delta_2R:28515481-28531112
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 11 | 16 | 0 |
| dead | 39 | 12 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 33 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 10 | 15 | 2 |
| dead | 39 | 12 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 33 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 10 | 14 | 3 |
| dead | 39 | 12 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 33 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 9 | 14 | 4 |
| dead | 39 | 12 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 33 | 17 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 10 | 14 | 3 |
| dead | 38 | 13 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 33 | 17 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 9 | 14 | 4 |
| dead | 37 | 14 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 34 | 16 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 34 | 16 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 9 | 14 | 4 |
| dead | 36 | 15 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 33 | 17 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 22 | 5 | 0 |
| dead | 36 | 14 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 8 | 15 | 4 |
| dead | 35 | 16 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 21 | 6 | 0 |
| dead | 36 | 14 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 8 | 15 | 4 |
| dead | 35 | 15 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 21 | 6 | 0 |
| dead | 35 | 15 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 7 | 16 | 4 |
| dead | 34 | 15 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 21 | 6 | 0 |
| dead | 35 | 15 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 9 | 11 | 7 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 21 | 6 | 0 |
| dead | 35 | 15 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 33 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 7 | 13 | 7 |
| dead | 29 | 18 | 4 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 3 | 0 |
| dead | 33 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 21 | 6 | 0 |
| dead | 36 | 14 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 4 | 14 | 9 |
| dead | 27 | 17 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 20 | 7 | 0 |
| dead | 36 | 14 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 3 | 15 | 9 |
| dead | 25 | 19 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 23 | 4 | 0 |
| dead | 32 | 17 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 20 | 7 | 0 |
| dead | 38 | 12 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 7 | 12 | 8 |
| dead | 28 | 18 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 19 | 8 | 0 |
| dead | 39 | 11 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 11 | 9 | 7 |
| dead | 30 | 16 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 17 | 10 | 0 |
| dead | 38 | 12 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 13 | 11 | 3 |
| dead | 35 | 12 | 4 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 14 | 12 | 1 |
| dead | 38 | 12 | 1 |
Baguida_gambiae_PM_X:15411876-15495650
Baguida_gambiae_PM_X:9165646-9222299
Baguida_gambiae_PM_X:9222298-9273975
Baguida_gambiae_PM_X:9273975-9317640
Baguida_gambiae_PM_X:9317639-9346605
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 17 | 14 | 4 |
| dead | 13 | 12 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 11 | 0 |
| dead | 12 | 16 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 20 | 11 | 4 |
| dead | 24 | 5 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 6 | 13 | 16 |
| dead | 9 | 13 | 8 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 10 | 1 |
| dead | 10 | 14 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 16 | 13 | 6 |
| dead | 13 | 15 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 10 | 1 |
| dead | 10 | 14 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 10 | 1 |
| dead | 10 | 14 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 20 | 11 | 4 |
| dead | 19 | 11 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 10 | 1 |
| dead | 11 | 14 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 19 | 14 | 2 |
| dead | 22 | 8 | 0 |
Korle-Bu_coluzzii_PM_2R:38097626-38111826
Korle-Bu_coluzzii_PM_2R:54371673-54397846
Korle-Bu_coluzzii_PM_3R:28482794-28505651
Korle-Bu_coluzzii_PM_3R:28505651-28533744
Korle-Bu_coluzzii_PM_3R:28563392-28595112
Korle-Bu_coluzzii_PM_3R:2929236-2946500
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 30 | 22 | 5 |
| dead | 34 | 9 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 34 | 20 | 3 |
| dead | 14 | 28 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 34 | 19 | 4 |
| dead | 40 | 8 | 0 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 39 | 17 | 1 |
| dead | 41 | 6 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 37 | 17 | 3 |
| dead | 15 | 29 | 4 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 26 | 24 | 7 |
| dead | 31 | 16 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 39 | 15 | 3 |
| dead | 40 | 7 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 20 | 27 | 10 |
| dead | 20 | 25 | 3 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 38 | 17 | 2 |
| dead | 18 | 25 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 38 | 16 | 3 |
| dead | 41 | 6 | 1 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 26 | 7 |
| dead | 7 | 27 | 14 |
Madina_gambiae_PM_2R:54255612-54278008
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 31 | 7 | 0 |
| dead | 14 | 12 | 1 |
Obuasi_gambiae_PM_2R:3474360-3509400
Obuasi_gambiae_PM_3L:30477135-30487616
Obuasi_gambiae_PM_3L:30487615-30497759
Obuasi_gambiae_PM_3L:30497758-30506894
Obuasi_gambiae_PM_3L:30506893-30516797
Obuasi_gambiae_PM_3L:30534828-30545854
Obuasi_gambiae_PM_3L:30554459-30562573
Obuasi_gambiae_PM_3L:30562572-30578511
Obuasi_gambiae_PM_3L:30578511-30587941
Obuasi_gambiae_PM_3L:30587941-30597762
Obuasi_gambiae_PM_3L:30597761-30607138
Obuasi_gambiae_PM_3L:30607137-30617085
Obuasi_gambiae_PM_3L:30617085-30624950
Obuasi_gambiae_PM_3L:30624949-30635698
Obuasi_gambiae_PM_3L:30635698-30646602
Obuasi_gambiae_PM_3L:30646601-30657763
Obuasi_gambiae_PM_3L:30657762-30667355
Obuasi_gambiae_PM_3L:30667355-30678119
Obuasi_gambiae_PM_3L:30678119-30687769
Obuasi_gambiae_PM_3L:30687769-30697180
Obuasi_gambiae_PM_3R:48454456-48494640
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 1 | 2 | 51 |
| dead | 1 | 16 | 33 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 37 | 16 | 1 |
| dead | 17 | 28 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 33 | 20 | 1 |
| dead | 14 | 29 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 36 | 17 | 1 |
| dead | 13 | 31 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 35 | 19 | 0 |
| dead | 15 | 29 | 6 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 35 | 18 | 1 |
| dead | 15 | 31 | 4 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 36 | 17 | 1 |
| dead | 16 | 29 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 36 | 16 | 2 |
| dead | 16 | 29 | 5 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 35 | 17 | 2 |
| dead | 15 | 28 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 35 | 17 | 2 |
| dead | 15 | 28 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 35 | 17 | 2 |
| dead | 15 | 28 | 7 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 34 | 18 | 2 |
| dead | 15 | 27 | 8 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 33 | 18 | 3 |
| dead | 15 | 25 | 10 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 30 | 21 | 3 |
| dead | 10 | 28 | 12 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 30 | 21 | 3 |
| dead | 10 | 28 | 12 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 28 | 24 | 2 |
| dead | 11 | 29 | 10 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 28 | 24 | 2 |
| dead | 11 | 30 | 9 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 27 | 25 | 2 |
| dead | 10 | 31 | 9 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 26 | 26 | 2 |
| dead | 11 | 29 | 10 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 26 | 26 | 2 |
| dead | 9 | 30 | 11 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 24 | 24 | 6 |
| dead | 39 | 9 | 2 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 43 | 10 | 1 |
| dead | 38 | 9 | 3 |
| phenotype | wt | het | hom |
|---|---|---|---|
| alive | 44 | 10 | 0 |
| dead | 39 | 10 | 1 |